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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Keywords HAS EXACT PHRASE "IMMUNE SYSTEM/Viral protein"

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Search Summary

This query matches 214 Structures.

Refinements

Structure Determination Methodology

experimental (214)

Scientific Name of Source Organism

	Homo sapiens (160)
	Severe acute respiratory syndrome coronavirus 2 (86)
	Mus musculus (42)
	Human immunodeficiency virus 1 (35)
	Macaca mulatta (9)
	Influenza A virus (8)
	Hepacivirus hominis (7)
	dengue virus type 2 (6)
	Hepatitis C virus (isolate H) (4)
	Oryctolagus cuniculus (4)

More...

Taxonomy

	Eukaryota (214)
	Riboviria (189)
	Duplodnaviria (9)
	Monodnaviria (4)
	Varidnaviria (4)
	Riboviria (RNA viruses and viroids) (3)

Experimental Method

	X-RAY DIFFRACTION (146)
	ELECTRON MICROSCOPY (68)

Polymer Entity Type

Protein (214)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (19)
	2.0 - 2.5 (53)
	2.5 - 3.0 (48)
	3.0 - 3.5 (48)
	3.5 - 4.0 (33)
	4.0 - 4.5 (8)
	> 4.5 (3)

Release Date

	2000 - 2004 (1)
	2005 - 2009 (5)
	2010 - 2014 (34)
	2015 - 2019 (18)
	2020 - 2024 (150)
	2025 - 2029 (6)

Enzyme Classification Name

	Hydrolases (3)
	Transferases (2)

Membrane Protein Annotation

OPM (1)

Symmetry Type

	Asymmetric (180)
	Cyclic (36)
	Tetrahedral (1)

SCOP Classification

	All beta proteins (54)
	Artifacts (16)
	Alpha and beta proteins (a+b) (23)
	Membrane and cell surface proteins and peptides (2)
	Small proteins (1)
	All alpha proteins (1)

AllSelected

1 to 25 of 214 Structures

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2DD8 \| pdb_00002dd8	Download File View File

Crystal Structure of SARS-CoV Spike Receptor-Binding Domain Complexed with Neutralizing Antibody

Prabakaran, P., Gan, J.H., Feng, Y., Zhu, Z.Y., Xiao, X.D., Ji, X., Dimitrov, D.S.

(2006) J Biological Chem 281: 15829-15836

Released	2006-04-04
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens Severe acute respiratory syndrome-related coronavirus
Macromolecule	IGG Heavy Chain (protein) IGG Light Chain (protein) Spike glycoprotein (protein)
Unique Ligands	NAG, PO4

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2FWO \| pdb_00002fwo	Download File View File

MHC Class I H-2Kd heavy chain in complex with beta-2microglobulin and peptide derived from influenza nucleoprotein

Mitaksov, V., Fremont, D.H.

(2006) J Biological Chem 281: 10618-10625

Released	2006-02-21
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Influenza A virus Mus musculus
Macromolecule	Beta-2-microglobulin (protein) H-2 class I histocompatibility antigen, K-D alpha chain (protein) TYQRTRALV peptide from Nucleoprotein (protein)

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2I9L \| pdb_00002i9l	Download File View File

Structure of Fab 7D11 from a neutralizing antibody against the poxvirus L1 protein

Su, H.P., Golden, J.W., Gittis, A.G., Moss, B., Hooper, J.W., Garboczi, D.N.

(2007) Virology 368: 331-341

Released	2007-09-18
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Mus musculus Vaccinia virus
Macromolecule	Antibody 7D11 heavy chain (protein) Antibody 7D11 light chain (protein) Virion membrane protein M25 (protein)
Unique Ligands	GOL

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2QHR \| pdb_00002qhr	Download File View File

Crystal structure of the 13F6-1-2 Fab fragment bound to its Ebola virus glycoprotein peptide epitope.

Lee, J.E., Kuehne, A., Abelson, D.M., Fusco, M.L., Hart, M.K., Saphire, E.O.

(2008) J Mol Biology 375: 202-216

Released	2008-01-22
Method	X-RAY DIFFRACTION 2 Å
Organisms	Mus musculus Zaire ebolavirus (strain Eckron-76)
Macromolecule	13F6-1-2 Fab fragment V lambda x light chain (protein) 13F6-1-2 Fab fragment heavy chain (protein) Envelope glycoprotein peptide (protein)

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2WY3 \| pdb_00002wy3	Download File View File

Structure of the HCMV UL16-MICB complex elucidates select binding of a viral immunoevasin to diverse NKG2D ligands

Mueller, S., Zocher, G., Steinle, A., Stehle, T.

(2010) PLoS Pathog 6: 723

Released	2010-02-02
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens Human herpesvirus 5 strain AD169
Macromolecule	MHC CLASS I POLYPEPTIDE-RELATED SEQUENCE B (protein) UNCHARACTERIZED PROTEIN UL16 (protein)
Unique Ligands	ACT, NAG, PEU

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2XQY \| pdb_00002xqy	Download File View File

CRYSTAL STRUCTURE OF PSEUDORABIES CORE FRAGMENT OF GLYCOPROTEIN H IN COMPLEX WITH FAB D6.3

Backovic, M., Dubois, R., Cockburn, J., Sharff, A., Vaney, M., Granzow, H., Klupp, B., Bricogne, G., Mettenleiter, T., Rey, F.

(2010) Proc Natl Acad Sci U S A 107: 22635

Released	2010-12-22
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Mus musculus Suid alphaherpesvirus 1
Macromolecule	A13-D6.3 MONOCLONAL ANTIBODY (protein) ENVELOPE GLYCOPROTEIN H (protein)
Unique Ligands	NAG
Unique branched monosaccharides	NAG

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2Y6S \| pdb_00002y6s	Download File View File

Structure of an Ebolavirus-protective antibody in complex with its mucin-domain linear epitope

Olal, D.O., Kuehne, A., Lee, J.E., Bale, S., Dye, J.M., Saphire, E.O.

(2012) J Virol 86: 2809

Released	2012-01-11
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Ebola virus - Zaire (1995) Mus musculus
Macromolecule	ENVELOPE GLYCOPROTEIN (protein) HEAVY CHAIN (protein) LIGHT CHAIN (protein)

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2YPL \| pdb_00002ypl	Download File View File

Structural features underlying T-cell receptor sensitivity to concealed MHC class I micropolymorphisms

Stewart-Jones, G.B., Simpson, P., van der Merwe, P.A., Easterbrook, P., McMichael, A.J., Rowland-Jones, S.L., Jones, E.Y., Gillespie, G.M.

(2012) Proc Natl Acad Sci U S A 109: E3483

Released	2012-11-28
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens Human immunodeficiency virus
Macromolecule	AGA T-CELL RECEPTOR ALPHA CHAIN (protein) AGA T-CELL RECEPTOR BETA CHAIN (protein) BETA-2-MICROGLOBULIN (protein) HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-57 ALPHA CHAIN (protein) KF11 P24 GAG PEPTIDE (protein)

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3CSY \| pdb_00003csy	Download File View File

Crystal structure of the trimeric prefusion Ebola virus glycoprotein in complex with a neutralizing antibody from a human survivor

Lee, J.E., Fusco, M.L., Hessell, A.J., Oswald, W.B., Burton, D.R., Saphire, E.O.

(2008) Nature 454: 177-182

Released	2008-07-08
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Ebola virus - Mayinga, Zaire, 1976 Homo sapiens
Macromolecule	Envelope glycoprotein GP1 (protein) Envelope glycoprotein GP2 (protein) Fab KZ52 heavy chain (protein) Fab KZ52 light chain (protein)
Unique branched monosaccharides	BMA, MAN, NAG

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3O41 \| pdb_00003o41	Download File View File

Crystal Structure of 101F Fab Bound to 15-mer Peptide Epitope

McLellan, J.S., Chen, M., Chang, J.S., Yang, Y., Kim, A., Graham, B.S., Kwong, P.D.

(2010) J Virol 84: 12236-12244

Released	2010-10-13
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Human respiratory syncytial virus A Mus musculus
Macromolecule	Fusion glycoprotein F1 (protein) Mouse monoclonal antibody 101F Fab heavy chain (protein) Mouse monoclonal antibody 101F Fab light chain (protein)
Unique Ligands	SO4

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3O45 \| pdb_00003o45	Download File View File

Crystal Structure of 101F Fab Bound to 17-mer Peptide Epitope

McLellan, J.S., Chen, M., Chang, J.S., Yang, Y., Kim, A., Graham, B.S., Kwong, P.D.

(2010) J Virol 84: 12236-12244

Released	2010-10-13
Method	X-RAY DIFFRACTION 2.872 Å
Organisms	Human respiratory syncytial virus A (strain A2) Mus musculus
Macromolecule	Fusion glycoprotein F1 (protein) Mouse monoclonal antibody 101F 101F Fab heavy chain (protein) Mouse monoclonal antibody 101F 101F Fab light chain (protein)
Unique Ligands	SO4

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3S88 \| pdb_00003s88	Download File View File

Crystal structure of Sudan Ebolavirus Glycoprotein (strain Gulu) bound to 16F6

Saphire, E.O., Dias, J.M., Bale, S.

(2011) Nat Struct Mol Biol 18: 1424-1427

Released	2011-12-07
Method	X-RAY DIFFRACTION 3.351 Å
Organisms	Mus musculus Sudan ebolavirus
Macromolecule	16F6 - Heavy chain (protein) 16F6 - Light chain (protein) Envelope glycoprotein (protein)
Unique branched monosaccharides	NAG

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3TYG \| pdb_00003tyg	Download File View File

Crystal structure of broad and potent HIV-1 neutralizing antibody PGT128 in complex with a glycosylated engineered gp120 outer domain with miniV3 (eODmV3)

Pejchal, R., Huang, P.S., Schief, W.R., Stanfield, R.L., Wilson, I.A.

(2011) Science 334: 1097-1103

Released	2011-10-19
Method	X-RAY DIFFRACTION 3.25 Å
Organisms	HIV-1 unknown group Homo sapiens
Macromolecule	Envelope glycoprotein gp160 (protein) PGT128 heavy chain, Ig gamma-1 chain C region (protein) PGT128 light chain, Ig lambda-2 chain C regions (protein)
Unique branched monosaccharides	BMA, MAN, NAG

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3VE0 \| pdb_00003ve0	Download File View File

Crystal structure of Sudan Ebolavirus Glycoprotein (strain Boniface) bound to 16F6

Saphire, E.O., Bale, S., Dias, J.M.

(2012) Viruses 4: 447-470

Released	2012-04-18
Method	X-RAY DIFFRACTION 3.353 Å
Organisms	Mus musculus Sudan virus - Boniface, Sudan,1976
Macromolecule	16F6 Antibody chain A (protein) 16F6 Antibody chain B (protein) Envelope glycoprotein (protein)
Unique branched monosaccharides	MAN, NAG

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3VRL \| pdb_00003vrl	Download File View File

Crystal structure of BMJ4 p24 capsid protein in complex with A10F9 Fab

Gu, Y., Cao, F., Li, S., Yuan, Y.A., Xia, N.

To be published

Released	2013-04-17
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Human immunodeficiency virus 1 Mus musculus
Macromolecule	A10F9 Fab heavy chain (protein) A10F9 Fab light chain (protein) Gag protein (protein)

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3ZTJ \| pdb_00003ztj	Download File View File

Structure of influenza A neutralizing antibody selected from cultures of single human plasma cells in complex with human H3 Influenza haemagglutinin.

Voss, J.E., Vachieri, S.G., Gamblin, S.J., Collins, P.J., Haire, L.F., Skehel, J.J.

(2011) Science 333: 850

Released	2011-08-10
Method	X-RAY DIFFRACTION 3.41 Å
Organisms	Homo sapiens Influenza A virus (A/Aichi/2/1968(H3N2))
Macromolecule	FI6V3 ANTIBODY HEAVY CHAIN (protein) FI6V3 ANTIBODY LIGHT CHAIN (protein) HEMAGGLUTININ HA1 CHAIN (protein) HEMAGGLUTININ HA2 CHAIN (protein)
Unique Ligands	NAG
Unique branched monosaccharides	BMA, NAG

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4BZ1 \| pdb_00004bz1	Download File View File

Structure of dengue virus EDIII in complex with Fab 3e31

Li, J., Watterson, D., Chang, C.W., Li, X.Q., Ericsson, D.J., Qiu, L.W., Cai, J.P., Chen, J., Fry, S.R., Cooper, M.A., Che, X.Y., Young, P.R., Kobe, B.

To be published

Released	2014-08-13
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Mus musculus dengue virus type 4
Macromolecule	ENVELOPE PROTEIN (protein) FAB 3E31 HEAVY CHAIN (protein) FAB 3E31 LIGHT CHAIN (protein)
Unique Ligands	CL, GOL, NA, ZN

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4DGV \| pdb_00004dgv	Download File View File

Structure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the broadly neutralizing antibody HCV1, P2(1) form

Kong, L., Wilson, I.A., Law, M.

(2012) Proc Natl Acad Sci U S A 109: 9499-9504

Released	2012-05-23
Method	X-RAY DIFFRACTION 1.805 Å
Organisms	Hepacivirus hominis Homo sapiens
Macromolecule	E2 peptide (protein) HCV1 Heavy Chain (protein) HCV1 Light Chain (protein)
Unique Ligands	K, NA

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4DGY \| pdb_00004dgy	Download File View File

Structure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the broadly neutralizing antibody HCV1, C2 form

Kong, L., Wilson, I.A., Law, M.

(2012) Proc Natl Acad Sci U S A 109: 9499-9504

Released	2012-05-23
Method	X-RAY DIFFRACTION 1.798 Å
Organisms	Hepacivirus hominis Homo sapiens
Macromolecule	E2 peptide (protein) HCV1 Heavy Chain (protein) HCV1 Light Chain (protein)
Unique Ligands	CL, GOL

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4ETQ \| pdb_00004etq	Download File View File

Vaccinia virus D8L IMV envelope protein in complex with Fab of murine IgG2a LA5

Matho, M.H., Zajonc, D.M.

(2012) J Virol 86: 8050-8058

Released	2012-06-06
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Mus musculus Vaccinia virus
Macromolecule	IMV membrane protein (protein) anti-vaccinia D8L antigen murine monoclonal IgG2a antibody LA5, heavy chain (protein) anti-vaccinia D8L antigen murine monoclonal IgG2a antibody LA5, light chain (protein)
Unique Ligands	CL, EDO, GOL, SCN

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4FFY \| pdb_00004ffy	Download File View File

Crystal structure of DENV1-E111 single chain variable fragment bound to DENV-1 DIII, strain 16007.

Austin, S.K., Nelson, C.A., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID)

(2012) PLoS Pathog 8: e1002930-e1002930

Released	2012-06-20
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Mus musculus dengue virus type 1
Macromolecule	DENV1-E111 single chain variable fragment (heavy chain) (protein) DENV1-E111 single chain variable fragment (light chain) (protein) envelope glycoprotein (protein)
Unique Ligands	CL, GOL, SO4

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4FFZ \| pdb_00004ffz	Download File View File

Crystal Structure of DENV1-E111 fab fragment bound to DENV-1 DIII (Western Pacific-74 strain).

Austin, S.K., Nelson, C.A., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID)

(2012) PLoS Pathog 8: e1002930-e1002930

Released	2012-06-27
Method	X-RAY DIFFRACTION 3.8 Å
Organisms	Dengue virus 1 Nauru/West Pac/1974 Mus musculus
Macromolecule	DENV1-E111 fab fragment (heavy chain) (protein) DENV1-E111 fab fragment (light chain) (protein) Envelope protein E (protein)

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4HKJ \| pdb_00004hkj	Download File View File

Structure of Cowpox CPXV203 in complex with MHCI (H-2Kb)

McCoy IV, W.H., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID)

(2012) PLoS Biol 10: e1001432-e1001432

Released	2012-11-14
Method	X-RAY DIFFRACTION 3 Å
Organisms	Cowpox virus (Brighton Red) Gallus gallus Homo sapiens Mus musculus
Macromolecule	Beta-2-microglobulin (protein) CPXV203 protein (protein) H-2 class I histocompatibility antigen, K-B alpha chain (protein) Ovalbumin (protein)

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4HPO \| pdb_00004hpo	Download File View File

Crystal structure of RV144-elicited antibody CH58 in complex with V2 peptide

McLellan, J.S., Gorman, J., Haynes, B.F., Kwong, P.D.

(2013) Immunity 38: 176-186

Released	2013-02-06
Method	X-RAY DIFFRACTION 1.694 Å
Organisms	Homo sapiens Human immunodeficiency virus 1
Macromolecule	CH58 Fab heavy chain (protein) CH58 Fab light chain (protein) Envelope glycoprotein gp160 (protein)
Unique branched monosaccharides	FUC, NAG

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4HPY \| pdb_00004hpy	Download File View File

Crystal structure of RV144-elicited antibody CH59 in complex with V2 peptide

McLellan, J.S., Gorman, J., Haynes, B.F., Kwong, P.D.

(2013) Immunity 38: 176-186

Released	2013-02-06
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Homo sapiens Human immunodeficiency virus 1
Macromolecule	CH59 Fab heavy chain (protein) CH59 Fab light chain (protein) Envelope glycoprotein gp160 (protein)
Unique Ligands	GOL

1 to 25 of 214 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

2DD8 | pdb_00002dd8

2FWO | pdb_00002fwo

2I9L | pdb_00002i9l

2QHR | pdb_00002qhr

2WY3 | pdb_00002wy3

2XQY | pdb_00002xqy

2Y6S | pdb_00002y6s

2YPL | pdb_00002ypl

3CSY | pdb_00003csy

3O41 | pdb_00003o41

3O45 | pdb_00003o45

3S88 | pdb_00003s88

3TYG | pdb_00003tyg

3VE0 | pdb_00003ve0

3VRL | pdb_00003vrl

3ZTJ | pdb_00003ztj

4BZ1 | pdb_00004bz1

4DGV | pdb_00004dgv

4DGY | pdb_00004dgy

4ETQ | pdb_00004etq

4FFY | pdb_00004ffy

4FFZ | pdb_00004ffz

4HKJ | pdb_00004hkj

4HPO | pdb_00004hpo

4HPY | pdb_00004hpy